Co-evolutionary analysis suggests a role for TLR9 in papillomavirus restriction

Upon infection, DNA viruses can be sensed by pattern recognition receptors (PRRs) leading to the activation of type I and III interferons, aimed at blocking infection. Therefore, viruses must inhibit these signaling pathways, avoid being detected, or both. Papillomavirus virions are trafficked from early endosomes to the Golgi apparatus and wait for the onset of mitosis to complete nuclear entry. This unique subcellular trafficking strategy avoids detection by cytoplasmic PRRs, a property that may contribute to establishment of infection. However, as the capsid uncoats within acidic endosomal compartments, the viral DNA may be exposed to detection by toll-like receptor (TLR) 9. In this study we characterize two new papillomaviruses from bats and use molecular archeology to demonstrate that their genomes altered their nucleotide composition to avoid detection by TLR9, providing evidence that TLR9 acts as a PRR during papillomavirus infection. Furthermore, we demonstrate that TLR9, like other components of the innate immune system, is under evolutionary selection in bats, providing the first direct evidence for co-evolution between papillomaviruses and their hosts

Smoking, self-regulation and moral positioning: a focus group study with British smokers from a disadvantaged community

Smoking in many Western societies has become a both moral aand health issue in recent years, but little is known about how smokers position themselves and regulate their behaviour in this context. In this article, we report the findings from a study investigating how smokers from an economically disadvantaged community in the East Midlands (UK) respond to concerns about the health impact of smoking on others. We conducted ten focus group (FG) discussions with mixed groups (by smoking status and gender; N = 58 participants) covering a range of topics, including smoking norms, self-regulation, and smoking in diverse contexts. We transcribed all FG discussions before analysing the data using techniques from discourse anlysis. Smokers in general positioned themselves as socially responsible smokers and morally upstanding citizens. This position was bolstered in two main ways: ‘everyday accommodation', whereby everyday efforts to accommodate the needs of non-smokers were referenced, and ‘taking a stand', whereby proactive interventions to prevent smoking in (young) others were cited. We suggest that smoking cessation campaigns could usefully be informed by this ethic of care for others

Regionally consistent Western North America paleomagnetic directions from 15 to 35 ka: Assessing chronology and uncertainty with paleosecular variation (PSV) stratigraphy

New Paleomagnetic Secular Variation (PSV) data from Fish Lake, Utah, USA, along with previously published regional records, allow us to build an independently dated Western North America PSV stack (WNAM17) from about 35 to 15 ka that quantifies dating and paleomagnetic uncertainties. In February 2014, we recovered a composite 11-m-long sediment record from Fish Lake, Utah that retrieved glacially influenced and post-glacial sediments. Computed tomography (CT) scans and magnetic susceptibility were used to build a precise depth scale, while radiocarbon dating of terrestrial macrofossils and tephrostratigraphy provide tight age-control. Glacially influenced sediments have well-defined characteristic remanent magnetizations with all maximum angular deviation values < 5 degrees, resolving a record of Late Pleistocene PSV. Comparison to the PSV records at Bear Lake, Utah/Idaho, USA and Bessette Creak, British Columbia, Canada, which also contain terrestrial material radiocarbon age-control points, allow us to develop the WNAM17 PSV stack which considers both dating and magnetic acquisition uncertainties. We utilize a regional PSV chronostratigraphic modeling approach to assign chronology and uncertainty to the PSV signal and to evaluate the fidelity of age-control points at the site level that are difficult to objectively evaluate otherwise. The greatest strength of our age-depth model is that by approaching chronostratigraphy from a regional perspective, assuming a common geomagnetic signal, we can address sources of geologic uncertainty that would be difficult to quantify using only one site. We illustrate the potential stratigraphic opportunities using the WNAM17 PSV template through assessing the timing of paleoenvironmental and paleomagnetic events in Western North America, including the timing of glaciations in the Fish Lake and Bear Lake catchments and the stratigraphic context for the Late Pleistocene geomagnetic excursion recorded at Mono Lake. (C) 2018 Elsevier Ltd. All rights reserved

Genome-wide meta-analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits

Few genome-wide association studies (GWAS) account for environmental exposures, like smoking, potentially impacting the overall trait variance when investigating the genetic contribution to obesity-related traits. Here, we use GWAS data from 51,080 current smokers and 190,178 nonsmokers (87% European descent) to identify loci influencing BMI and central adiposity, measured as waist circumference and waist-to-hip ratio both adjusted for BMI. We identify 23 novel genetic loci, and 9 loci with convincing evidence of gene-smoking interaction (GxSMK) on obesity-related traits. We show consistent direction of effect for all identified loci and significance for 18 novel and for 5 interaction loci in an independent study sample. These loci highlight novel biological functions, including response to oxidative stress, addictive behaviour, and regulatory functions emphasizing the importance of accounting for environment in genetic analyses. Our results suggest that tobacco smoking may alter the genetic susceptibility to overall adiposity and body fat distribution.Peer reviewe

The recovery of European freshwater biodiversity has come to a halt

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss1. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity2. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.N. Kaffenberger helped with initial data compilation. Funding for authors and data collection and processing was provided by the EU Horizon 2020 project eLTER PLUS (grant agreement no. 871128); the German Federal Ministry of Education and Research (BMBF; 033W034A); the German Research Foundation (DFG FZT 118, 202548816); Czech Republic project no. P505-20-17305S; the Leibniz Competition (J45/2018, P74/2018); the Spanish Ministerio de Economía, Industria y Competitividad—Agencia Estatal de Investigación and the European Regional Development Fund (MECODISPER project CTM 2017-89295-P); Ramón y Cajal contracts and the project funded by the Spanish Ministry of Science and Innovation (RYC2019-027446-I, RYC2020-029829-I, PID2020-115830GB-100); the Danish Environment Agency; the Norwegian Environment Agency; SOMINCOR—Lundin mining & FCT—Fundação para a Ciência e Tecnologia, Portugal; the Swedish University of Agricultural Sciences; the Swiss National Science Foundation (grant PP00P3_179089); the EU LIFE programme (DIVAQUA project, LIFE18 NAT/ES/000121); the UK Natural Environment Research Council (GLiTRS project NE/V006886/1 and NE/R016429/1 as part of the UK-SCAPE programme); the Autonomous Province of Bolzano (Italy); and the Estonian Research Council (grant no. PRG1266), Estonian National Program ‘Humanitarian and natural science collections’. The Environment Agency of England, the Scottish Environmental Protection Agency and Natural Resources Wales provided publicly available data. We acknowledge the members of the Flanders Environment Agency for providing data. This article is a contribution of the Alliance for Freshwater Life (www.allianceforfreshwaterlife.org).Peer reviewe

Ancient DNA provides evidence of 27,000-year-old papillomavirus infection and long-term codivergence with rodents

The long-term evolutionary history of many viral lineages is poorly understood. Novel sources of ancient DNA combined with phylogenetic analyses can provide insight into the time scale of virus evolution. Here we report viral sequences from ancient North American packrat middens. We screened samples up to 27,000-years old and found evidence of papillomavirus (PV) infection in Neotoma cinerea (Bushy-tailed packrat). Phylogenetic analysis placed the PV sequences in a clade with other previously published PV sequences isolated from rodents. Concordance between the host and virus tree topologies along with a correlation in branch lengths suggests a shared evolutionary history between rodents and PVs. Based on host divergence times, PVs have likely been circulating in rodents for at least 17 million years. These results have implications for our understanding of PV evolution and for further research with ancient DNA from Neotoma middens.National Science Foundation [DGE-1143953]; David and Lucile Packard FoundationOpen Access Journal.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Recommending rides: psychometric profiling in the theme park

This paper presents a study intended to inform the design of a recommender system for theme park rides. It examines the efficacy of psychometric testing for profiling theme park visitors, with the aim of establishing a set of measures to be included in a visitor profile intended for use in a collaborative recommender system. Results presented in this paper highlight the predictive value of a number of psychometric measures, including two drawn from the ―Big Five‖ personality inventory, and one drawn from the ―Sensation Seeking Scale‖. The paper discusses general research challenges associated with the integration of psychometric testing into recommender systems, and describes planned future work on a theme park recommender system

FIGuRE 1 in Inordinate Fondness Multiplied And Redistributed: The Number Of Species On Earth And The New Pie Of Life

FIGuRE 1. TRADITIoNAL AND NEw EsTIMATEs oF THE PIE oF LIFE The pie on the left shows a traditional estimate of the relative richness of different groups of organisms based on numbers of described species (Wilson 1992), the middle shows an estimate based on projected richness of different groups (Mora et al. 2011), and the pie on the right shows estimates based on the projected richness of different groups in the present study. The pie on the right is estimated based on Scenario 1 (Table 1), but other scenarios and assumptions give very similar estimates of the relative richness of different groups (Tables 1 – 4), even as total species richness changes. See the online edition for a color version of this figure

The emergence of SARS-CoV-2 in Europe and North America.

Accurate understanding of the global spread of emerging viruses is critically important for public health responses and for anticipating and preventing future outbreaks. Here, we elucidate when, where and how the earliest sustained SARS-CoV-2 transmission networks became established in Europe and North America. Our results suggest that rapid early interventions successfully prevented early introductions of the virus into Germany and the US from taking hold. Other, later introductions of the virus from China to both Italy and to Washington State founded the earliest sustained European and North America transmission networks. Our analyses demonstrate the effectiveness of public health measures in preventing onward transmission and show that intensive testing and contact tracing could have prevented SARS-CoV-2 from becoming established.status: Published onlin